Mixed messages: re-initiation factors regulate translation of animal mRNAs

When ribosomes encounter upstream open reading frames (uORFs) during scanning of the 5' untranslated region (5' UTR), translation of the downstream ORF requires re-initiation. In a recent paper in Nature, Schleich et al. describe metazoan factors which specifically promote re-initiation

Pinwheel stabilization by ocular dominance segregation

We present an analytical approach for studying the coupled development of ocular dominance and orientation preference columns. Using this approach we demonstrate that ocular dominance segregation can induce the stabilization and even the production of pinwheels by their crystallization in two types of periodic lattices. Pinwheel crystallization depends on the overall dominance of one eye over the other, a condition that is fulfilled during early cortical development. Increasing the strength of inter-map coupling induces a transition from pinwheel-free stripe solutions to intermediate and high pinwheel density states.Comment: 10 pages, 4 figure

Cellular Structures for Computation in the Quantum Regime

We present a new cellular data processing scheme, a hybrid of existing cellular automata (CA) and gate array architectures, which is optimized for realization at the quantum scale. For conventional computing, the CA-like external clocking avoids the time-scale problems associated with ground-state relaxation schemes. For quantum computing, the architecture constitutes a novel paradigm whereby the algorithm is embedded in spatial, as opposed to temporal, structure. The architecture can be exploited to produce highly efficient algorithms: for example, a list of length N can be searched in time of order cube root N.Comment: 11 pages (LaTeX), 3 figure

Understanding visual map formation through vortex dynamics of spin Hamiltonian models

The pattern formation in orientation and ocular dominance columns is one of the most investigated problems in the brain. From a known cortical structure, we build spin-like Hamiltonian models with long-range interactions of the Mexican hat type. These Hamiltonian models allow a coherent interpretation of the diverse phenomena in the visual map formation with the help of relaxation dynamics of spin systems. In particular, we explain various phenomena of self-organization in orientation and ocular dominance map formation including the pinwheel annihilation and its dependency on the columnar wave vector and boundary conditions.Comment: 4 pages, 15 figure

Tracing tumorigenesis in a solid tumor model at single-cell resolution

Characterizing the complex composition of solid tumors is fundamental for understanding tumor initiation, progression and metastasis. While patient-derived samples provide valuable insight, they are heterogeneous on multiple molecular levels, and often originate from advanced tumor stages. Here, we use single-cell transcriptome and epitope profiling together with pathway and lineage analyses to study tumorigenesis from a developmental perspective in a mouse model of salivary gland squamous cell carcinoma. We provide a comprehensive cell atlas and characterize tumor-specific cells. We find that these cells are connected along a reproducible developmental trajectory: initiated in basal cells exhibiting an epithelial-to-mesenchymal transition signature, tumorigenesis proceeds through Wnt-differential cancer stem cell-like subpopulations before differentiating into luminal-like cells. Our work provides unbiased insights into tumor-specific cellular identities in a whole tissue environment, and emphasizes the power of using defined genetic model systems

Tension Dynamics and Linear Viscoelastic Behavior of a Single Semiflexible Polymer Chain

We study the dynamical response of a single semiflexible polymer chain based on the theory developed by Hallatschek et al. for the wormlike-chain model. The linear viscoelastic response under oscillatory forces acting at the two chain ends is derived analytically as a function of the oscillation frequency . We shall show that the real part of the complex compliance in the low frequency limit is consistent with the static result of Marko and Siggia whereas the imaginary part exhibits the power-law dependence +1/2. On the other hand, these compliances decrease as the power law -7/8 for the high frequency limit. These are different from those of the Rouse dynamics. A scaling argument is developed to understand these novel results.Comment: 23 pages, 6 figure

Conditional Quantum Dynamics and Logic Gates

Quantum logic gates provide fundamental examples of conditional quantum dynamics. They could form the building blocks of general quantum information processing systems which have recently been shown to have many interesting non--classical properties. We describe a simple quantum logic gate, the quantum controlled--NOT, and analyse some of its applications. We discuss two possible physical realisations of the gate; one based on Ramsey atomic interferometry and the other on the selective driving of optical resonances of two subsystems undergoing a dipole--dipole interaction.Comment: 5 pages, RevTeX, two figures in a uuencoded, compressed fil

A census of cell types and paracrine interactions in colorectal cancer

In colorectal cancer, oncogenic mutations transform a hierarchically organized and homeostatic epithelium into invasive cancer tissue. To define differences in cellular composition between the normal colon and colorectal cancer, and to map potential cellular interactions between tumor cells and their microenvironment, we profiled transcriptomes of >50,000 single cells from tumors and matched normal tissues of eight colorectal cancer patients. We find that tumor formation is accompanied by changes in epithelial, immune and stromal cell compartments in all patients. In the epithelium, we identify a continuum of five tumor-specific stem cell and progenitor-like populations, and persistent multilineage differentiation. We find multiple stromal and immune cell types to be consistently expanded in tumor compared to the normal colon, including cancer-associated fibroblasts, pericytes, monocytes, macrophages and a subset of T cells. We identify epithelial tumor cells and cancer-associated fibroblasts as relevant for assigning colorectal cancer consensus molecular subtypes. Our survey of growth factors in the tumor microenvironment identifies cell types responsible for increased paracrine EGFR, MET and TGF-β signaling in tumor tissue compared to the normal colon. We show that matched colorectal cancer organoids retain cell type heterogeneity, allowing to define a distinct differentiation trajectory encompassing stem and progenitor-like tumor cells. In summary, our single-cell analyses provide insights into cell types and signals shaping colorectal cancer cell plasticity

Coordinated optimization of visual cortical maps (I) Symmetry-based analysis

In the primary visual cortex of primates and carnivores, functional architecture can be characterized by maps of various stimulus features such as orientation preference (OP), ocular dominance (OD), and spatial frequency. It is a long-standing question in theoretical neuroscience whether the observed maps should be interpreted as optima of a specific energy functional that summarizes the design principles of cortical functional architecture. A rigorous evaluation of this optimization hypothesis is particularly demanded by recent evidence that the functional architecture of OP columns precisely follows species invariant quantitative laws. Because it would be desirable to infer the form of such an optimization principle from the biological data, the optimization approach to explain cortical functional architecture raises the following questions: i) What are the genuine ground states of candidate energy functionals and how can they be calculated with precision and rigor? ii) How do differences in candidate optimization principles impact on the predicted map structure and conversely what can be learned about an hypothetical underlying optimization principle from observations on map structure? iii) Is there a way to analyze the coordinated organization of cortical maps predicted by optimization principles in general? To answer these questions we developed a general dynamical systems approach to the combined optimization of visual cortical maps of OP and another scalar feature such as OD or spatial frequency preference.Comment: 90 pages, 16 figure

Generation of maximum spin entanglement induced by cavity field in quantum-dot systems

Equivalent-neighbor interactions of the conduction-band electron spins of quantum dots in the model of Imamoglu et al. [Phys. Rev. Lett. 83, 4204 (1999)] are analyzed. Analytical solution and its Schmidt decomposition are found and applied to evaluate how much the initially excited dots can be entangled to the remaining dots if all of them are initially disentangled. It is demonstrated that the perfect maximally entangled states (MES) can only be generated in the systems of up to 6 dots with a single dot initially excited. It is also shown that highly entangled states, approximating the MES with a good accuracy, can still be generated in systems of odd number of dots with almost half of them being excited. A sudden decrease of entanglement is observed by increasing the total number of dots in a system with a fixed number of excitations.Comment: 6 pages, 7 figures, to appear in Phys. Rev.